The storyline directly follows DC Universe #0 after the conclusion of the 51-issue Countdown to Final Crisis weekly limited series.[3] Promotion about the limited series describes its story as "the day evil won". The series deals with alien villain Darkseid's plot to overthrow reality, and the subsequent death and corruption of various DC characters and their universe.

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Final Crisis came out of several ideas Grant Morrison had when he returned to DC Comics in 2003. Morrison said, "I pitched a huge crossover event called Hypercrisis, which didn’t happen for various reasons. Some of Hypercrisis went into Seven Soldiers, some went into All-Star Superman, some went into 52 and some of it found a home in Final Crisis."[4] According to Grant Morrison, work finally began on Final Crisis #1 in early 2006, with the intention of the series being a thematic and literal sequel to Seven Soldiers and 52, two projects that Morrison was heavily involved in at the time.[5]

References to Infinite Crisis as the "middle Crisis"[6] gave readers the impression there would be at least one additional major follow-up to the original Crisis on Infinite Earths. A May 2007 teaser poster confirmed this speculation with the tagline: "Heroes die. Legends live forever."

Final Crisis was preceded by Countdown, a year-long weekly series which was meant as a follow-up to 52. Halfway through, the series was renamed Countdown to Final Crisis. However, the artwork met with delays.[citation needed] To keep the release on schedule, Countdown wrapped with issue #1 and its planned final issue (#0) was revamped as a 50 cent one-shot special called DC Universe #0. Besides hyping upcoming storylines such as "Batman R.I.P." and "Blackest Night," the issue was narrated by Barry Allen and featured Libra leading a group of super-villains in prayer for the "god of evil", Darkseid. The result is, as described by Morrison, that "we’re watching him fall back through the present, into the past of Seven Soldiers where he finally comes to rest in the body of 'Boss Dark Side’, the gangster from that story."[5]

To help readers identify events pertinent to Final Crisis and other major DCU events as the crossover approached, a "Sightings" cover banner appeared on various DC comics as "signposts, marking important storybeats and moments throughout the DC Universe."[7] The first such headers appeared on Justice League of America (vol. 2) #21 and Action Comics #866, respectively (the JLA issue featured Libra's return and his recruiting of the Human Flame).

The original intent was for Jones to pencil the whole series. Due to delays, however, Carlos Pacheco drew issues #4-6 with Jones, and issue 7 was drawn entirely by Doug Mahnke. Jones said that “Any problems completing the series are my own. I love Doug Mahnke’s art, and he would have probably been a better choice to draw this series in the first place.”[8]

In addition to the core limited series the larger storyline includes a number of tie-ins, including one-shots and limited series.

The one-shots comprise "Requiem,"[9] "Resist,"[10] "Secret Files" and "Submit". Also "Rage of the Red Lanterns" is the start of a storyline of the same name, that picks up on events in "Green Lantern: Secret Origin" and continues in Green Lantern #36-38. It starts as a tie-in because, according to writer Geoff Johns, "events in Final Crisis have motivated the Guardians to proceed further with their attempted containment of the light".[11]

Following the final battle of the New Gods, the spirit of the lord of evil, Darkseid, tumbles through time itself, coming to rest on Earth, where it, along with the spirits of the other evil gods of Apokolips, manifests itself in the body of a human being. Darkseid's "fall" has sundered reality, creating a singularity at the heart of creation, into which all of space and time are slowly being drawn, setting the stage for the evil god's final victory, to be claimed in his inevitable death. Through his agent Libra, he arranges for a huge army of super villains to be gathered, who capture and murder the Martian Manhunter as the opening salvo of the conflict. Coinciding with the Manhunter's death is the arrival on Earth of Nix Uotan, an exiled member of the cosmic Monitors, who has been sentenced to become human as punishment for failure in his duties.

Following the trail of a group of missing child prodigies, detective Dan Turpin discovers the dying body of Darkseid's son, Orion. The Justice League of America liaise with the Green Lantern Corps to investigate the murder, deducing the cause of death to be a bullet of Radion—a substance toxic to New Gods—fired backwards through time from the future. New God Granny Goodness, possessing the body of Green Lantern Kraken, stymies the investigation by framing Hal Jordan for the murder; when Batman deduces her true identity, she captures him and teleports him to Command D, a government bio-chemical weapons facility beneath the city of Blüdhaven that has also fallen under the control of Darkseid's minions. Slowly becoming aware of the threat the evil gods pose, Alan Scott enacts "Article X", a super hero draft, that readies Earth's metahuman forces for the coming war.

With Batman and Jordan removed from play, the New Gods continue to eliminate the greatest threats to Darkseid's plan. Wonder Woman is infected by the Morticoccous bacteria by a Desaad-possessed Mary Marvel while investigating Blüdhaven. Superman departs for the future in order to obtain a cure for Lois Lane when a bomb in the Daily Planet building mortally wounds her. The Silver Age Flash, Barry Allen, is resurrected from within the Speed Force by powers unknown, but then races back in time alongside Wally West, attempting to outrun the Black Racer, the Death of the New Gods, and stop the bullet that will kill Orion.

Turpin's search for the missing children leads him to the Dark Side Club, where he is confronted by Darkseid's human host, Boss Dark Side. The evil god transfers his essence into Turpin's body and brings him to Command D, where the detective is subjected to bio-genetic restructuring to transform his body into a replica of Darkseid's original form. Concurrently, Darkseid's agents release the Anti-Life Equation through all of Earth's communications networks, spreading it across the entire planet. The two Flashes, having failed to prevent Orion's death, emerge from the time stream one month after the equation's release, and discover that the minds of nearly the entire population have fallen under Darkseid's control, with its super-human victims having been transformed into a military force of "Justifiers".

With the help of the Tattooed Man, the Super Young Team and former allies of the New Gods of New GenesisShilo Norman and Sonny Sumo, the small cells of super heroes who have managed to resist the equation discover a possible salvation: a symbol from the alphabet of the New Gods that will break the equation's control over minds, which was gifted to the cave-boy Anthro by Metron in prehistoric times. Meanwhile, a huge battle erupts between the superheroes and the Justifiers in Blüdhaven, during which the equation-controlled Wonder Woman infects the heroes with Morticoccous, which strips the heroes of their powers. However, the loss of these troops is soon mitigated by the turning of Libra's Justifiers, control over whom is usurped by Lex Luthor and Doctor Sivana so they can help defeat Darkseid. These twists and turns are observed by Nix Uotan, whose powers and memories of his true nature are unlocked with the help of Metron and a mysterious ape-like figure in a robe.

Escaping confinement in Command D, Batman uses the radion bullet to mortally wound Darkseid, before the dark god uses his Omega Beams to kill Batman. Superman returns to the present and tears Command D apart to recover Batman's corpse, and faces off against Darkseid as the Flashes come racing into Blüdhaven, the Black Racer hot on their heels. As the heroes reach super-luminal velocity, time warps around the Flashes, creating the temporal eddy into which Darkseid fires the bullet, sending it back in time to kill Orion. Outpacing Omega Beams fired from the eyes of the humans in Darkseid's thrall, the Flashes lead both the beams and the Black Racer straight to Darkseid, finishing the job Batman had begun and bringing the touch of death to the god of evil. Simultaneously, The Ray traces the Metron symbol across the face of the Earth in beams of light, liberating all those under the equation's control; the freed Wonder Woman uses her lasso of truth to release Darkseid's consciousness from Turpin's body.

Although physically bested, Darkseid's dying essence is still dragging all of reality into nothingness along with it. Time and space break down as the effect worsens, until eventually, only Superman is left in the darkness at the end of creation, struggling to complete a copy of the "Miracle Machine," a wish-granting machine shown to him by Brainiac 5 during his trip to the future. Darkseid's essence re-emerges to claim the machine, but Superman destroys him for good by using the last of his super-powered breath to sing, countering the vibrational frequency of Darkseid's life-force.

With Darkseid's end, however, the evil behind evils emerges: Mandrakk, the Dark Monitor, fallen father of Nix Uotan, who waits at the end of all things to consume what remains. Superman uses the solar energy in his own cells to power the Miracle Machine, and makes a wish that is granted by the appearance of an army of Supermen from all across the multiverse, including one modeled on U.S. PresidentBarack Obama.[15] Nix Uotan joins the clash, using his Monitor powers to summon the Green Lantern Corps, the Zoo Crew, the Super Young Team, the armies of Heaven itself, and more for a final battle with Mandrakk that culminates in the Corps spearing him with a stake made of pure light and created by the combined energy of their rings. The heroes drag Earth out of the black hole that is Darkseid, and Nix Uotan returns to being human as the other Monitors cease to exist in accordance with the wish Superman had made: a wish for a happy ending.

In the distant past, Anthro dies of old age in a cave. His body is discovered by Bruce Wayne — not dead, but sent back in time by the Omega Beams—who picks up where Anthro left off, drawing a bat symbol on the cave wall.

The first issue of Final Crisis went on sale May 28, 2008.[16]Final Crisis was seven oversized issues released over nine months starting in May 2008.[17] Morrison explained that the order stories in the main series and tie-ins written by him unfold is Final Crisis #1-3, Superman Beyond #1-2, Final Crisis: Submit, Final Crisis #4–5, Batman #682–683, and finally Final Crisis #6–7.[4]

Several one-shots and mini-series have been released as tie-ins to Final Crisis:[18] three series run in parallel to the main one and the one-shot, DC Universe: Last Will and Testament, was planned to fit in the 'break' between Final Crisis #3 and #4.[19]

Morrison, who wrote one of the "final" Batman stories in "Batman R.I.P.," stated, "First it's R.I.P., and we'll see how that winds up for Batman. Then the two-parter mentioned (Batman #682-683) goes through Batman's whole career, in a big summing up of everything that also ties directly into Final Crisis. And Final Crisis is where we see the final fate of Batman."[20]

While not an official tie-in, the Terror Titans mini-series takes place during the events of Final Crisis and deals heavily with the Dark Side Club and the Anti-Life Equation.

In a move Dan DiDio described as "inspirationally tied to Final Crisis," in early 2009 the villains took over the main DC Universe titles and some were featured in "Faces of Evil," a series of one-shots, all designed to examine the question "What happens when evil wins?"[23]

Blackest Knight, the third story arc in Grant Morrison's Batman and Robin, deals with the revelation of the truth regarding the supposed "body" of Bruce Wayne left behind at the conclusion of Final Crisis #6.[34]

In the 1997-1998 JLA story-arc "Rock Of Ages" a future where Darkseid had enslaved the Human race using the Anti-Life Equation was shown. This story-arc resembles some similarities to events shown in Final Crisis and was also written by Grant Morrison.